On 25/10/2011 4:20 AM, EGY wrote:
Thanks for taking the time to answer, but I think my wording may have confused my
question. I shouldn't have used the word box. Within the protein their are several
aromatic residues that interact with the small molecule cation. I would like to preserve
these interactions throughout the simulations. Is it possible to "enhance"
these interactions, since there is no defined force constants that describes these
interactions?
Distance restraints are commonly used in proteins containing an unbound
ion. This can keep things in place, but there's no particular reason to
suppose it's a good model of something about which you care...
Mark
Thanks.
Egy
On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote:
EGY wrote:
I am interesting in modeling a small molecule ligand-protein complex that
involves a cationic ligand encapsulated by several aromatic residues that form
a box around the cation. However, md simulations result in the cation moving
outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain
the cation portion of the small molecule to within the aromatic box? Or is
there a better forcefield, which will take these interactions into
consideration.
More than likely you simply need to account for periodicity.
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
-Justin
Thanks.
Egy-- gmx-users mailing list gmx-users@gromacs.org
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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